The present application claims priority under 35 U.S.C. xc2xa7119 to German application 199 24 365.4, filed on May 27, 1999.
1. Field of the Invention
The invention provides nucleotide sequences coding for the accDA gene and a process for the preparation of L-amino acids, especially L-lysine, by fermentation using corynebacteria in which the accDA gene is amplified.
2. Background Information
L-Amino acids, especially L-lysine, are used in animal nutrition, in human medicine and in the pharmaceutical industry.
It is known that these amino acids are prepared by the fermentation of strains of corynebacteria, especially Corynebacterium glutamicum. Because of their great importance, attempts are constantly being made to improve the preparative processes. Improvements to the processes may relate to measures involving the fermentation technology, e.g. stirring and oxygen supply, or the composition of the nutrient media, e.g. the sugar concentration during fermentation, or the work-up to the product form, e.g. by ion exchange chromatography, or the intrinsic productivity characteristics of the microorganism itself.
The productivity characteristics of these microorganisms are improved by using methods of mutagenesis, selection and mutant choice to give strains which are resistant to antimetabolites, e.g. the lysine analog S-(2-aminoethyl)cysteine, or auxotrophic for amino acids of regulatory significance, and produce L-amino acids.
Methods of recombinant DNA technology have also been used for some years in order to improve L-amino acid-producing strains of Corynebacterium by amplifying individual amino acid biosynthesis genes and studying the effect on L-lysine production. Surveys of this subject have been published inter alia by Kinoshita (xe2x80x9cGlutamic Acid Bacteriaxe2x80x9d in: Biology of Industrial Microorganisms, Demain and Solomon (Eds.), Benjamin Cummings, London, UK, 1985, 115-142), Hilliger (BioTec 2, 40-44 (1991)), Eggeling (Amino Acids 6, 261-272 (1994)), Jetten and Sinskey (Critical Reviews in Biotechnology 15, 73-103 (1995)) and Sahm et al. (Annuals of the New York Academy of Science 782, 25-39 (1996)).
The enzyme acetyl-CoA carboxylase catalyzes the carboxylation of acetyl-CoA to malonyl-CoA. The enzyme from Escherichia coli consists of four subunits. The accB gene codes for biotin carboxyl carrier protein, the accC gene for biotin carboxylase and the accA and accD genes for transcarboxylase (Cronan and Rock, Biosynthesis of Membrane Lipids, in: Escherichia coli and Salmonella typhimurium (ed. F. C. Neidhardt), 1996, pp. 612-636, American Society for Microbiology). Because of the property of the enzyme to carboxylate acyl groups in the form of acyl-CoA, it is also called acyl-CoA carboxylase.
The nucleotide sequence of the accBC gene from Corynebacterium glutamicum has been determined by Jxc3xa4ger et al. (Archives of Microbiology 166, 76-82 (1996)) and is generally available from the data bank of the European Molecular Biologies Laboratories (EMBL, Heidelberg, Germany) under accession number U35023. The accBC gene codes for a subunit of acetyl-CoA carboxylase which carries a biotin carboxyl carrier protein domain and a biotin carboxylase domain.
The object which the inventors set themselves was to provide novel procedures for the improved preparation of L-amino acids, especially L-lysine, by fermentation.
L-Amino acids are used in animal nutrition, in human medicine and in the pharmaceutical industry. It is therefore of general interest to provide novel improved processes for the preparation of L-amino acids.
When L-lysine or lysine is mentioned in the following text, it is understood as meaning not only the base but also the salts, e.g. lysine monohydrochloride or lysine sulfate.
The invention provides a preferably recombinant DNA originating from Corynebacterium which is capable of replication in coryneform microorganisms and which at least contains the nucleotide sequence coding for the accDA gene shown in SEQ ID No. 1.
The invention also provides a DNA capable of replication, as claimed in claim 1, with:
(i) the nucleotide sequence shown in SEQ ID No. 1, or
(ii) at least one sequence corresponding to the sequence (i) within the region of degeneracy of the genetic code, or
(iii) at least one sequence hybridizing with the sequence complementary to the sequence (i) or (ii), and optionally
(vi) [sic] neutral sense mutations in (i).
The invention also provides coryneform microorganisms, especially of the genus Corynebacterium, transformed by the introduction of said DNA capable of replication.
The invention further relates to a process for the preparation of L-amino acids by fermentation using corynebacteria which, in particular, already produce the L-amino acids and in which the nucleotide sequences coding for the accDA gene are amplified and, in particular, overexpressed.
Finally, the invention also provides a process for the amplification of acyl-CoA carboxylase in corynebacteria by joint overexpression of the novel accDA gene according to the invention and the known accBC gene.
In this context the term xe2x80x9camplificationxe2x80x9d describes the increase in the intracellular activity, in a microorganism, of one or more enzymes which are coded for by the appropriate DNA, for example by increasing the copy number of the gene(s), using a strong promoter or using a gene coding for an appropriate enzyme with a high activity, and optionally combining these measures.
The microorganisms which the present invention provides can produce L-amino acids from glucose, sucrose, lactose, fructose, maltose, molasses, starch or cellulose or from glycerol and ethanol. Said microorganisms can be representatives of corynebacteria, especially of the genus Corynebacterium. The species Corynebacterium glutamicum may be mentioned in particular in the genus Corynebacterium, being known to those skilled in the art for its ability to produce L-amino acids.
Suitable strains of the genus Corynebacterium, especially of the species Corynebacterium glutamicum for example, are the known wild-type strains:
Corynebacterium glutamicum ATCC13032
Corynebacterium acetoglutamicum ATCC15806
Corynebacterium acetoacidophilum ATCC13870
Corynebacterium thermoaminogenes FERM BP-1539
Brevibacterium flavum ATCC14067
Brevibacterium lactofermentum ATCC13869 and
Brevibacterium divaricatum ATCC14020 and L-amino acid-producing mutants or strains prepared therefrom, for example:
Corynebacterium glutamicum FERM-P 1709
Brevibacterium flavum FERM-P 1708
Brevibacterium lactofermentum FERM-P 1712
Corynebacterium glutamicum FERM-P 6463 and
Corynebacterium glutamicum FERM-P 6464
The inventors have succeeded in isolating the novel accDA gene from C. glutamicum. The accDA gene or other genes are isolated from C. glutamicum by first constructing a gene library of this microrganism [sic] in E. coli. The construction of gene libraries is documented in generally well-known textbooks and handbooks. Examples which may be mentioned are the textbook by Winnacker entitled From Genes to Clones, Introduction to Gene Technology (Verlag Chemie, Weinheim, Germany, 1990) or the handbook by Sambrook et al. entitled Molecular Cloning, A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989). A very well-known gene library is that of the E. coli K-12 strain W3110 constructed by Kohara et al. (Cell 50, 495-508 (1987)) in xcex vectors. Bathe et al. (Molecular and General Genetics 252, 255-265 (1996)) describe a gene library of C. glutamicum ATCC13032 constructed using cosmid vector SuperCos I (Wahl et al., Proceedings of the National Academy of Sciences USA 84, 2160-2164 (1987)) in the E. coli K-12 strain NM554 (Raleigh et al., Nucleic Acids Research 16, 1563-1575 (1988)). Bxc3x6rmann et al. (Molecular Microbiology 6(3), 317-326) in turn describe a gene library of C. glutamicum ATCC13032 using cosmid pHC79 (Hohn and Collins, Gene 11, 291-298 (1980)). A gene library of C. glutamicum in E. coli can also be constructed using plasmids like pBR322 (Bolivar, Life Sciences 25, 807-818 (1979)) or pUC9 (Viera et al., Gene 19, 259-268 (1982)). Restriction- and recombination-defective E. coli strains are particularly suitable hosts, an example being the strain DH5xcex1mcr described by Grant et al. (Proceedings of the National Academy of Sciences USA 87, 4645-4649 (1990)). The long DNA fragments cloned using cosmids can then in turn be subcloned into common vectors suitable for sequencing, and subsequently sequenced, e.g. as described by Sanger et al. (Proceedings of the National [sic] of Sciences of the United States of America [sic] USA 74, 5463-5467 (1977)).
The novel DNA sequence from C. glutamicum coding for the accDA gene was obtained in this way and, as SEQ ID No. 1, is part of the present invention. The coding region (cds) of the accDA gene is shown in SEQ ID No. 2. The amino acid sequence of the corresponding protein was also derived from the present DNA sequence by the methods described above. The resulting amino acid sequence of the accDA gene product is shown in SEQ ID No. 3.
Coding DNA sequences which result from SEQ ID No. 1 due to the degeneracy of the genetic code are also part of the invention. Similarly, DNA sequences which hybridize with SEQ ID No. 1 or sections of SEQ ID No. 1 are part of the invention. Furthermore, conservative amino acid exchanges, e.g. the exchange of glycine for alanine or of aspartic acid for glutamic acid in proteins, are known to those skilled in the art as sense mutations, which do not cause a fundamental change in the activity of the protein, i.e. they are neutral. It is also known that changes at the N and/or C terminus of a protein do not substantially impair its function or can even stabilize it. Those skilled in the art will find information on this subject inter alia in Ben-Bassat et al. (Journal of Bacteriology 169, 751-757 (1987)), O""Regan et al. (Gene 77, 237-251 (1989)), Sahin-Toth et al. (Protein Sciences 3, 240-247 (1994)), Hochuli et al. (Bio/Technology 6, 1321-1325 (1988)) and well-known textbooks on genetics and molecular biology. Amino acid sequences which correspondingly result from SEQ ID No. 3 are also part of the invention.
The inventors have found that overexpression of the accDA genes in corynebacteria improves L-lysine production.
An overexpression can be achieved by increasing the copy number of the appropriate genes or mutating the promoter and regulatory region or the ribosome binding site located upstream from the structural gene. Expression cassettes incorporated upstream from the structural gene work in the same way. Inducible promoters additionally make it possible to increase the expression in the course of L-lysine production by fermentation. Measures for prolonging the life of the mRNA also improve the expression. Furthermore, the enzyme activity is also enhanced by preventing the degradation of the enzyme protein. The genes or gene constructs can either be located in plasmids of variable copy number or be integrated and amplified in the chromosome. Alternatively, it is also possible to achieve an overexpression of the genes in question by changing the composition of the media and the culture technique.
Those skilled in the art will find appropriate instructions inter alia in Martin et al. (Bio/Technology 5, 137-146 (1987)), Guerrero et al. (Gene 138, 35-41 (1994)), Tsuchiya and Morinaga (Bio/Technology 6, 428-430 (1988)), Eikmanns et al. (Gene 102, 93-98 (1991)), EP 0 472 869, U.S. Pat. No. 4,601,893, Schwarzer and Pxc3xchler (Bio/Technology 9, 84-87 (1991)), Reinscheid et al. (Applied and Environmental Microbiology 60, 126-132 (1994)), LaBarre et al. (Journal of Bacteriology 175, 1001-1007 (1993)), patent application WO 96/15246, Malumbres et al. (Gene 134, 15-24 (1993)), Japanese Offenlegungsschrift JP-A-10-229891, Jensen and Hammer (Biotechnology and Bioengineering 58, 191-195 (1998)), Makrides (Microbiological Reviews 60, 512-538 (1996)) and well-known textbooks on genetics and molecular biology.
An example of a plasmid by means of which the accDA gene can be overexpressed is pZ1accDA (FIG. 1), which is contained in the strain MH20-22B/pZlaccDA. Plasmid pZ1accDA is an E. coli-C. glutamicum shuttle vector which carries the accDA gene and is based on plasmid pZ1 (Menkel et al., Applied and Environmental Microbiology 55(3), 684-688 (1989)). Other plasmid vectors capable of replication in C. glutamicum, e.g. pEKEx1 (Eikmanns et al., Gene 102, 93-98 (1991)) or pZ8-1 (EP 0 375 889), can be used in the same way.
The inventors have also found that overexpression of the known accBC gene in addition to the novel accDA gene according to the invention in corynebacteria improves acyl-CoA carboxylase production. An example of a plasmid by means of which the accDA gene and the accBC gene can be jointly overexpressed is pEK0accBCaccDA (FIG. 2). Plasmid pEK0accBCaccDA is an E. colixe2x80x94C. glutamicum shuttle vector which carries the accBC and accDA genes and is based on plasmid pEK0 (Eikmanns et al., Gene 102, 93-98 (1991)). Other plasmid vectors capable of replication in C. glutamicum, e.g. pEKEx1 (Eikmanns et al., Gene 102, 93-35 98 (1991)) or pZ8-1 (EP 0 375 889), can be used in the same way.
In addition, it can be advantageous for L-amino acid production to overexpress not only the accDA gene but also one or more enzymes of the biosynthetic pathway. Thus it is possible, for example for the preparation of L-lysine,
simultaneously to overexpress the dapA gene coding for dihydrodipicolinate synthase (EP-B 0 197 335), or
simultaneously to amplify a DNA fragment conferring S-(2-aminoethyl)cysteine resistance (EP-A 0 088 166).
Furthermore, it can be advantageous for the production of L-amino acids, especially L-lysine, to switch off undesirable secondary reactions as well as overexpress the accDA gene (Nakayama: xe2x80x9cBreeding of Amino Acid Producing Micro-organismsxe2x80x9d in: Overproduction of Microbial Products, Krumphanzl, Sikyta, Vanek (eds.), Academic Press, London, UK, 1982).
The microorganisms prepared according to the invention can be cultivated for L-lysine production continuously or discontinuously by the batch process, the fed batch process or the repeated fed batch process. A summary of known cultivation methods is provided in the textbook by Chmiel (Bioprozesstechnik 1. Einfxc3xchrung in die Bioverfahrenstechnik (Bioprocess Technology 1. Introduction to Bioengineering) (Gustav Fischer Verlag, Stuttgart, 1991)) or in the textbook by Storhas (Bioreaktoren und periphere Einrichtungen (Bioreactors and Peripheral Equipment) (Vieweg Verlag, Brunswick/Wiesbaden, 1994)).
The culture medium to be used must appropriately meet the demands of the particular strains. Descriptions of culture media for various microorganisms can be found in the handbook xe2x80x9cManual of Methods for General Bacteriologyxe2x80x9d of the American Society for Bacteriology (Washington D.C., USA, 1981). Carbon sources which can be used are sugars and carbohydrates, e.g. glucose, sucrose, lactose, fructose, maltose, molasses, starch and cellulose, oils and fats, e.g. soya oil, sunflower oil, groundnut oil and coconut fat, fatty acids, e.g. palmitic acid, stearic acid and linoleic acid, alcohols, e.g. glycerol and ethanol, and organic acids, e.g. acetic acid. These substances can be used individually or as a mixture. Nitrogen sources which can be used are organic nitrogen-containing compounds such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soybean flour and urea, or inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate and ammonium nitrate. The nitrogen sources can be used individually or as a mixture. Phosphorus sources which can be used are phosphoric acid, potassium dihydrogenphosphate or dipotassium hydrogenphosphate or the corresponding sodium salts. The culture medium must also contain metal salts, e.g. magnesium sulfate or iron sulfate, which are necessary for growth. Finally, essential growth-promoting substances such as amino acids and vitamins can be used in addition to the substances mentioned above. Suitable precursors can also be added to the culture medium. Said feed materials can be added to the culture all at once or fed in appropriately during cultivation.
The pH of the culture is controlled by the appropriate use of basic compounds such as sodium hydroxide, potassium hydroxide, ammonia or aqueous ammonia, or acid compounds such as phosphoric acid or sulfuric acid. Foaming can be controlled using antifoams such as fatty acid polyglycol esters. The stability of plasmids can be maintained by adding suitable selectively acting substances, e.g. antibiotics, to the medium. Aerobic conditions are maintained by introducing oxygen or oxygen-containing gaseous mixtures, e.g. air, into the culture. The temperature of the culture is normally 20xc2x0 C. to 45xc2x0 C. and preferably 25xc2x0 C. to 40xc2x0 C. The culture is continued until formation of the desired L-amino acid has reached a maximum. This objective is normally achieved within 10 hours to 160 hours.
L-Lysine can be analyzed takes place [sic] by means of anion exchange chromatography followed by ninhydrin derivatization, as described by Spackman et al. (Analytical Chemistry 30, 1190 (1958)).
The following microorganisms have been deposited in the Deutsche Sammlung fxc3xcr Mikrorganismen [sic] und Zellkulturen (German Collection of Microrganisms [sic] and Cell Cultures (DSMZ), Brunswick, Germany) under the terms of the Budapest Treaty:
Corynebacterium glutamicum strain DSM5715/pZ1accDA as DSM12785
Corynebacterium glutamicum strain DSM5715/pEK0accBCaccDA as DSM12787
The process according to the invention is used for the preparation of L-amino acids, especially L-aspartic acid, L-asparagine, L-homoserine, L-threonine, L-isoleucine and L-methionine, by the fermentation of corynebacteria. It is used particularly for the preparation of L-lysine.